Hey all,
I'm currently running highly multiplexed runs on a Nextseq 550 and I've come into the problem where a library submitted to me has an average 950bp length and has been shown to cluster extremely inefficiently (i.e. only 10% of the reads loaded for QC sequencing were returned pass filtered). The clients are now requesting about 40% of a mid output runs worth of data to account for the inefficiency of their library (they expect to get back only 10% of the data again). I'm worried about the downstream effects of running this inefficient pool on the run as a whole, since many other collaborators and data from our own lab will be on this run.
I'm currently running highly multiplexed runs on a Nextseq 550 and I've come into the problem where a library submitted to me has an average 950bp length and has been shown to cluster extremely inefficiently (i.e. only 10% of the reads loaded for QC sequencing were returned pass filtered). The clients are now requesting about 40% of a mid output runs worth of data to account for the inefficiency of their library (they expect to get back only 10% of the data again). I'm worried about the downstream effects of running this inefficient pool on the run as a whole, since many other collaborators and data from our own lab will be on this run.
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